Data

Tools

Indexes

Applications

Experiments

Open Source Science

scDD

R package to identify genes with differential distributions in single-cell RNA-seq

https://github.com/kdkorthauer/scdd

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 13 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.0%) to scientific vocabulary

Keywords from Contributors

bioconductor-package single-cell-rna-seq human-cell-atlas core-package bioinformatics bioconductor proteomics mass-spectrometry gene rna-seq
Last synced: 10 months ago · JSON representation

Repository

R package to identify genes with differential distributions in single-cell RNA-seq

Basic Info
  • Host: GitHub
  • Owner: kdkorthauer
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 10.2 MB
Statistics
  • Stars: 32
  • Watchers: 5
  • Forks: 15
  • Open Issues: 0
  • Releases: 0
Created over 10 years ago · Last pushed over 4 years ago

https://github.com/kdkorthauer/scDD/blob/master/ 

# scDD: An R package to identify differentially distributed genes in scRNA-seq 

## Installation 
The Bioconductor landing page is 
[https://bioconductor.org/packages/scDD](https://bioconductor.org/packages/scDD).
To install, make sure you have the current version of Bioconductor, and 
use the following commands:

```R
install.packages("BiocManager")
BiocManager::install("scDD")
```


## Quick Start
For examples and tips on using the package, please see the vignette PDF 
[here](http://bioconductor.org/packages/devel/bioc/vignettes/scDD/inst/doc/scDD.pdf)
which you can alternatively bring up by typing 

```R
browseVignettes("scDD")
```

after installing and loading the package into R.  

## Getting Help
Please send bug reports and feature requests by sending a message to Bioconductor
Support at [https://support.bioconductor.org](https://support.bioconductor.org)
or by opening a new issue on 
[this page](https://github.com/kdkorthauer/scDD/issues)

## Citation
Please cite the following publication if you use scDD in your work:
> Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, 
Kendziorski C. A statistical approach for identifying differential 
distributions in single-cell RNA-seq experiments. Genome Biology. 
2016 Oct 25;17(1):222. 
[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y)

You can obtain this citation within R by typing

```R
citation("scDD")
```

Owner

  • Name: Keegan Korthauer
  • Login: kdkorthauer
  • Kind: user
  • Location: Vancouver, BC | Canada
  • Company: University of British Columbia and BC Children's Hospital Research Institute

Assistant Professor, University of British Columbia | Investigator, BC Children's Hospital Research Institute

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 232
  • Total Committers: 13
  • Avg Commits per committer: 17.846
  • Development Distribution Score (DDS): 0.228
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kdkorthauer k****r@g****m 179
Keegan Korthauer k****n@j****u 16
Nitesh Turaga n****a@g****m 12
k.korthauer k****r@b****8 12
Herve Pages h****s@f****g 2
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Hervé Pagès h****b@g****m 1
Alan O'Callaghan a****n@o****m 1
mtmorgan@fhcrc.org m****n@f****g@b****8 1
Martin Morgan m****n@f****g 1
Kayla-Morrell k****l@r****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 2 fredhutch.org: 1 jimmy.harvard.edu: 1

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 22,055 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: scDD

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

  • Versions: 3
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 22,055 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 13.2%
Downloads: 39.7%
Maintainers (1)
keegan@stat.ubc.ca
Last synced: over 1 year ago

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • BiocParallel * imports
  • EBSeq * imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • arm * imports
  • fields * imports
  • ggplot2 * imports
  • grDevices * imports
  • graphics * imports
  • mclust * imports
  • outliers * imports
  • scran * imports
  • stats * imports
  • BiocStyle * suggests
  • gridExtra * suggests
  • knitr * suggests